Challenges of Integrative Disease Modeling in Alzheimer's Disease

Dementia-related diseases like Alzheimer's Disease (AD) have a tremendous social and economic cost. A deeper understanding of its underlying pathophysiologies may provide an opportunity for earlier detection and therapeutic intervention. Previous approaches for characterizing AD were targeted at single aspects of the disease. Yet, due to the complex nature of AD, the success of these approaches was limited. However, in recent years, advancements in integrative disease modeling, built on a wide range of AD biomarkers, have taken a global view on the disease, facilitating more comprehensive analysis and interpretation. Integrative AD models can be sorted in two primary types, namely hypothetical models and data-driven models. The latter group split into two subgroups: (i) Models that use traditional statistical methods such as linear models, (ii) Models that take advantage of more advanced artificial intelligence approaches such as machine learning. While many integrative AD models have been published over the last decade, their impact on clinical practice is limited. There exist major challenges in the course of integrative AD modeling, namely data missingness and censoring, imprecise human-involved priori knowledge, model reproducibility, dataset interoperability, dataset integration, and model interpretability. In this review, we highlight recent advancements and future possibilities of integrative modeling in the field of AD research, showcase and discuss the limitations and challenges involved, and finally, propose avenues to address several of these challenges.

[1]  Henrik Zetterberg,et al.  Determining cut-points for Alzheimer's disease biomarkers: statistical issues, methods and challenges. , 2012, Biomarkers in medicine.

[2]  Anil Rao,et al.  Classification of Alzheimer's Disease from structural MRI using sparse logistic regression with optional spatial regularization , 2011, 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

[3]  Sébastien Ourselin,et al.  Multiple Orderings of Events in Disease Progression , 2015, IPMI.

[4]  Raul Rodriguez-Esteban,et al.  Biocuration with insufficient resources and fixed timelines , 2015, Database J. Biol. Databases Curation.

[5]  Diego Castillo-Barnes,et al.  Studying the Manifold Structure of Alzheimer's Disease: A Deep Learning Approach Using Convolutional Autoencoders , 2020, IEEE Journal of Biomedical and Health Informatics.

[6]  C. Jack,et al.  Alzheimer's Disease Neuroimaging Initiative , 2008 .

[7]  Arthur W. Toga,et al.  Practical management of heterogeneous neuroimaging metadata by global neuroimaging data repositories , 2012, Front. Neuroinform..

[8]  T. Tombaugh Test-retest reliable coefficients and 5-year change scores for the MMSE and 3MS. , 2005, Archives of clinical neuropsychology : the official journal of the National Academy of Neuropsychologists.

[9]  Ernesto Fedele,et al.  The Amyloid Cascade Hypothesis in Alzheimer’s Disease: It’s Time to Change Our Mind , 2017, Current neuropharmacology.

[10]  Ronald C Petersen,et al.  New criteria for Alzheimer's disease: which, when and why? , 2015, Brain : a journal of neurology.

[11]  Jonathan R. Walsh,et al.  Machine learning for comprehensive forecasting of Alzheimer’s Disease progression , 2018, Scientific Reports.

[12]  Sebastien Ourselin,et al.  Uncovering the heterogeneity and temporal complexity of neurodegenerative diseases with Subtype and Stage Inference , 2017, bioRxiv.

[13]  M W Weiner,et al.  The relative efficiency of time-to-threshold and rate of change in longitudinal data. , 2011, Contemporary clinical trials.

[14]  Daoqiang Zhang,et al.  Tree-Guided Sparse Coding for Brain Disease Classification , 2012, MICCAI.

[15]  Mingshan Wang,et al.  Publication Trends for Alzheimer's Disease Worldwide and in China: A 30-Year Bibliometric Analysis , 2019, Front. Hum. Neurosci..

[16]  Eric E. Smith,et al.  Determining the impact of psychosis on rates of false-positive and false-negative diagnosis in Alzheimer's disease , 2017, Alzheimer's & Dementia.

[17]  Mladen Konecki,et al.  Mind map generator software model with text mining algorithm , 2011, Proceedings of the ITI 2011, 33rd International Conference on Information Technology Interfaces.

[18]  G. B. Frisoni,et al.  The dynamics of Alzheimer's disease biomarkers in the Alzheimer's Disease Neuroimaging Initiative cohort , 2010, Neurobiology of Aging.

[19]  Francisco M. Couto,et al.  Text Mining for Bioinformatics Using Biomedical Literature , 2019, Encyclopedia of Bioinformatics and Computational Biology.

[20]  Gokul Prabhakaran,et al.  Analysis of Structure and Cost in an American Longitudinal Study of Alzheimer's Disease , 2018 .

[21]  Alind Gupta,et al.  Bayesian Networks for Risk Prediction Using Real-World Data: A Tool for Precision Medicine. , 2019, Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research.

[22]  David Gomez-Cabrero,et al.  Data integration in the era of omics: current and future challenges , 2014, BMC Systems Biology.

[23]  Neil P. Oxtoby,et al.  Imaging plus X: multimodal models of neurodegenerative disease , 2017, Current opinion in neurology.

[24]  Jing Ning,et al.  Non‐parametric tests for right‐censored data with biased sampling , 2010, Journal of the Royal Statistical Society. Series B, Statistical methodology.

[25]  D. Delis,et al.  Quantification of five neuropsychological approaches to defining mild cognitive impairment. , 2009, The American journal of geriatric psychiatry : official journal of the American Association for Geriatric Psychiatry.

[26]  Pamela C. Heaton,et al.  Impact of the Food and Drug Administration’s antipsychotic black box warning on psychotropic drug prescribing in elderly patients with dementia in outpatient and office-based settings , 2012, Alzheimer's & Dementia.

[27]  Henrik Zetterberg,et al.  Effect of ponezumab on CSF biomarkers: Pooled analysis of phase IIa studies in subjects with mild-to-moderate Alzheimer's disease , 2012, Alzheimer's & Dementia.

[28]  Daniela Stan Raicu,et al.  Automatic extraction of informal topics from online suicidal ideation , 2018, BMC Bioinformatics.

[29]  Martin Hofmann-Apitius,et al.  Towards a Pathway Inventory of the Human Brain for Modeling Disease Mechanisms Underlying Neurodegeneration. , 2016, Journal of Alzheimer's disease : JAD.

[30]  J. Trojanowski,et al.  Integration and relative value of biomarkers for prediction of MCI to AD progression: Spatial patterns of brain atrophy, cognitive scores, APOE genotype and CSF biomarkers , 2013, NeuroImage: Clinical.

[31]  Sébastien Ourselin,et al.  An event-based model for disease progression and its application in familial Alzheimer's disease and Huntington's disease , 2012, NeuroImage.

[32]  Howard Aizenstein,et al.  Why we need two cutoffs for amyloid imaging: Early versus Alzheimer's-like amyloid-positivity , 2012, Alzheimer's & Dementia.

[33]  Benjamin M. Gyori,et al.  From word models to executable models of signaling networks using automated assembly , 2017, bioRxiv.

[34]  Nicholas Ostler,et al.  Corpus Design Criteria , 1992 .

[35]  M. Jorge Cardoso,et al.  Accurate multimodal probabilistic prediction of conversion to Alzheimer's disease in patients with mild cognitive impairment☆ , 2013, NeuroImage: Clinical.

[36]  Roy W Jones,et al.  On the path to 2025: understanding the Alzheimer’s disease continuum , 2017, Alzheimer's Research & Therapy.

[37]  Wenrui Hao,et al.  Computational Causal Modeling of the Dynamic Biomarker Cascade in Alzheimer's Disease , 2019, Comput. Math. Methods Medicine.

[38]  Martin Hofmann-Apitius,et al.  A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders , 2019, bioRxiv.

[39]  Meemansa Sood,et al.  Variational Autoencoder Modular Bayesian Networks (VAMBN) for Simulation of Heterogeneous Clinical Study Data , 2019, bioRxiv.

[40]  A. Fagan,et al.  Guidelines for the standardization of preanalytic variables for blood-based biomarker studies in Alzheimer's disease research , 2015, Alzheimer's & Dementia.

[41]  Vikas Singh,et al.  MKL for Robust Multi-modality AD Classification , 2009, MICCAI.

[42]  Nick C Fox,et al.  Clinical and biomarker changes in dominantly inherited Alzheimer's disease. , 2012, The New England journal of medicine.

[43]  T. Gale,et al.  Sex differences in cognitive impairment in Alzheimer's disease. , 2016, World journal of psychiatry.

[44]  Matthew L Senjem,et al.  Shapes of the trajectories of 5 major biomarkers of Alzheimer disease. , 2012, Archives of neurology.

[45]  Cynthia Rudin,et al.  Stop explaining black box machine learning models for high stakes decisions and use interpretable models instead , 2018, Nature Machine Intelligence.

[46]  H. Hu Victor,et al.  Demographic and clinical characteristics. , 2016 .

[47]  Denise C. Park,et al.  Toward defining the preclinical stages of Alzheimer’s disease: Recommendations from the National Institute on Aging-Alzheimer's Association workgroups on diagnostic guidelines for Alzheimer's disease , 2011, Alzheimer's & Dementia.

[48]  A. Baghestani,et al.  How to control confounding effects by statistical analysis , 2012, Gastroenterology and hepatology from bed to bench.

[49]  Anne M. Fagan,et al.  CSF Biomarkers of Alzheimer’s Disease: Impact on Disease Concept, Diagnosis, and Clinical Trial Design , 2014 .

[50]  C. Jack,et al.  Evidence for ordering of Alzheimer disease biomarkers. , 2011, Archives of neurology.

[51]  KongFatt Wong-Lin,et al.  A hybrid computational approach for efficient Alzheimer’s disease classification based on heterogeneous data , 2018, Scientific Reports.

[52]  Amy P. Abernethy,et al.  Harnessing the Power of Real‐World Evidence (RWE): A Checklist to Ensure Regulatory‐Grade Data Quality , 2017, Clinical pharmacology and therapeutics.

[53]  H. Benali,et al.  Support vector machine-based classification of Alzheimer’s disease from whole-brain anatomical MRI , 2009, Neuroradiology.

[54]  Tim Schultz,et al.  Disease progression model in subjects with mild cognitive impairment from the Alzheimer's disease neuroimaging initiative: CSF biomarkers predict population subtypes. , 2013, British journal of clinical pharmacology.

[55]  Christoforos Hadjichrysanthou,et al.  A Systematic Review of Longitudinal Studies Which Measure Alzheimer’s Disease Biomarkers , 2017, Journal of Alzheimer's disease : JAD.

[56]  M. Hofmann-Apitius,et al.  From integrative disease modeling to predictive, preventive, personalized and participatory (P4) medicine , 2013, EPMA Journal.

[57]  Magda Tsolaki,et al.  The interactive effect of demographic and clinical factors on hippocampal volume: A multicohort study on 1958 cognitively normal individuals , 2017, Hippocampus.

[58]  Jonathan A C Sterne,et al.  Accounting for missing data in statistical analyses: multiple imputation is not always the answer , 2019, International journal of epidemiology.

[59]  Mark Singh,et al.  Prioritization of Free-Text Clinical Documents: A Novel Use of a Bayesian Classifier , 2015, JMIR medical informatics.

[60]  C. Jack,et al.  Tracking pathophysiological processes in Alzheimer's disease: an updated hypothetical model of dynamic biomarkers , 2013, The Lancet Neurology.

[61]  Ainhoa Berciano-Alcaraz,et al.  A computational approach of , 2010 .

[62]  Daniel C Alexander,et al.  Data-driven models of dominantly-inherited Alzheimer’s disease progression , 2018, bioRxiv.

[63]  Jon Neville,et al.  Accelerating drug development for Alzheimer's disease through the use of data standards , 2017, Alzheimer's & dementia.

[64]  R. Kolamunnage-Dona,et al.  Time-dependent ROC curve analysis in medical research: current methods and applications , 2017, BMC Medical Research Methodology.

[65]  S. Resnick,et al.  Midlife adiposity predicts earlier onset of Alzheimer’s dementia, neuropathology and presymptomatic cerebral amyloid accumulation , 2015, Molecular Psychiatry.

[66]  Nick C. Fox,et al.  Data-driven models of dominantly-inherited Alzheimer’s disease progression , 2018 .

[67]  Julia Moeller,et al.  A word on standardization in longitudinal studies: don't , 2015, Front. Psychol..

[68]  Danilo Bzdok,et al.  Classical Statistics and Statistical Learning in Imaging Neuroscience , 2016, Front. Neurosci..

[69]  Demetrius J Porche,et al.  Precision Medicine Initiative , 2015, American journal of men's health.

[70]  Timothy J. Hohman,et al.  Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk , 2019, Nature Genetics.

[71]  Bernhard Hemmer,et al.  Consensus guidelines for lumbar puncture in patients with neurological diseases , 2017, Alzheimer's & dementia.

[72]  Clifford R Jack,et al.  Testing the Right Target and Right Drug at the Right Stage , 2011, Science Translational Medicine.

[73]  Isabelle Boutron,et al.  Misrepresentation and distortion of research in biomedical literature , 2018, Proceedings of the National Academy of Sciences.

[74]  Michel Thiebaut de Schotten,et al.  Biomarker-guided clustering of Alzheimer's disease clinical syndromes , 2019, Neurobiology of Aging.

[75]  David T. Jones,et al.  Defining imaging biomarker cut points for brain aging and Alzheimer's disease , 2017, Alzheimer's & Dementia.

[76]  Genetic,et al.  Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing , 2019, Nature Genetics.

[77]  Randall J Bateman,et al.  Dominantly Inherited Alzheimer Network: facilitating research and clinical trials , 2013, Alzheimer's Research & Therapy.

[78]  K. Blennow,et al.  Biomarkers for Alzheimer's disease: current status and prospects for the future , 2018, Journal of internal medicine.

[79]  Nathan Herrmann,et al.  Clinical practice guidelines for severe Alzheimer’s disease , 2007, Alzheimer's & Dementia.

[80]  D. Louis Collins,et al.  Early Prediction of Alzheimer's Disease Progression Using Variational Autoencoders , 2019, MICCAI.

[81]  C. Rowe,et al.  The Australian Imaging, Biomarkers and Lifestyle (AIBL) study of aging: methodology and baseline characteristics of 1112 individuals recruited for a longitudinal study of Alzheimer's disease , 2009, International Psychogeriatrics.

[82]  José Luis Molinuevo,et al.  European Prevention of Alzheimer’s Dementia Longitudinal Cohort Study (EPAD LCS): study protocol , 2018, BMJ Open.

[83]  Johann de Jong,et al.  Deep learning for clustering of multivariate clinical patient trajectories with missing values , 2019, GigaScience.

[84]  Christian Simon,et al.  BioReader: a text mining tool for performing classification of biomedical literature , 2019, BMC Bioinformatics.

[85]  Meng Wang,et al.  Demographic and clinical characteristics related to cognitive decline in Alzheimer disease in China , 2016, Medicine.

[86]  Eric Westman,et al.  The heterogeneity within Alzheimer's disease , 2018, Aging.

[87]  Nataša Pržulj,et al.  Methods for biological data integration: perspectives and challenges , 2015, Journal of The Royal Society Interface.

[88]  Christoph Bock,et al.  Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data , 2019, Genome Biology.

[89]  Christiane Reitz,et al.  Toward precision medicine in Alzheimer's disease. , 2016, Annals of translational medicine.

[90]  Bruno Vellas,et al.  Predictive Factors of Attrition in a Cohort of Alzheimer Disease Patients , 2008, Neuroepidemiology.

[91]  Holger Fröhlich,et al.  From hype to reality: data science enabling personalized medicine , 2018, BMC Medicine.

[92]  V. P. Gladun Hypothetical modeling: Methodology and application , 1997 .

[93]  B. Dubois,et al.  A Precision Medicine Initiative for Alzheimer’s disease: the road ahead to biomarker-guided integrative disease modeling , 2017, Climacteric : the journal of the International Menopause Society.

[94]  Michal Daszykowski,et al.  Revised DBSCAN algorithm to cluster data with dense adjacent clusters , 2013 .

[95]  Keith A. Johnson,et al.  A/T/N: An unbiased descriptive classification scheme for Alzheimer disease biomarkers , 2016, Neurology.

[96]  Clare E. Mackay,et al.  DEEP AND FREQUENT PHENOTYPING: A FEASIBILITY STUDY FOR EXPERIMENTAL MEDICINE IN DEMENTIA , 2017, Alzheimer's & Dementia.

[97]  Robert Tibshirani,et al.  Estimating the number of clusters in a data set via the gap statistic , 2000 .

[98]  Giovanni B. Frisoni,et al.  European Prevention of Alzheimer's Dementia Registry: Recruitment and prescreening approach for a longitudinal cohort and prevention trials , 2018, Alzheimer's & Dementia.

[99]  Daoqiang Zhang,et al.  Multimodal classification of Alzheimer's disease and mild cognitive impairment , 2011, NeuroImage.

[100]  C. Jack,et al.  Hypothetical model of dynamic biomarkers of the Alzheimer's pathological cascade , 2010, The Lancet Neurology.

[101]  Nick C Fox,et al.  Uncovering the heterogeneity and temporal complexity of neurodegenerative diseases with Subtype and Stage Inference , 2017, Nature Communications.

[102]  Carole A. Goble,et al.  State of the nation in data integration for bioinformatics , 2008, J. Biomed. Informatics.

[103]  Martin Hofmann-Apitius,et al.  Neuroimaging Feature Terminology: A Controlled Terminology for the Annotation of Brain Imaging Features , 2017, Journal of Alzheimer's disease : JAD.

[104]  Dragan Gamberger,et al.  Identification of clusters of rapid and slow decliners among subjects at risk for Alzheimer’s disease , 2017, Scientific Reports.

[105]  P. Austin An Introduction to Propensity Score Methods for Reducing the Effects of Confounding in Observational Studies , 2011, Multivariate behavioral research.

[106]  Vikas Singh,et al.  Predictive markers for AD in a multi-modality framework: An analysis of MCI progression in the ADNI population , 2011, NeuroImage.

[107]  Gang Chen,et al.  Staging Alzheimer’s Disease Risk by Sequencing Brain Function and Structure, Cerebrospinal Fluid, and Cognition Biomarkers , 2016, Journal of Alzheimer's disease : JAD.

[108]  Sylvain Paile,et al.  WHAT TO CONTROL , 2013 .

[109]  Paul M. Thompson,et al.  Multi-source learning with block-wise missing data for Alzheimer's disease prediction , 2013, KDD.

[110]  Charles DeCarli,et al.  Biological heterogeneity in ADNI amnestic mild cognitive impairment , 2014, Alzheimer's & Dementia.

[111]  Ryan M. Cassidy,et al.  Risk factors for amyloid positivity in older people reporting significant memory concern. , 2018, Comprehensive psychiatry.

[112]  Marilyn Albert,et al.  Variation in Variables that Predict Progression from MCI to AD Dementia over Duration of Follow-up. , 2013, American journal of Alzheimer's disease.

[113]  Nick C Fox,et al.  The clinical use of structural MRI in Alzheimer disease , 2010, Nature Reviews Neurology.

[114]  Pedro M. Domingos A few useful things to know about machine learning , 2012, Commun. ACM.

[115]  Mohammad Asif Emon,et al.  Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer’s Disease and Reconstruction of Relevant Biological Mechanisms , 2018, Scientific Reports.